EMBO Practical Course on Metabolomics Bioinformatics for Life Scientists
This course will provide an overview of key issues that affect metabolomics studies, handling dataset and procedures for the analysis of metabolomics data using bioinformatics tools. It will be delivered using a mixture of lectures, computer-based practical sessions and interactive discussions. The course will provide a platform for discussion of the key questions and challenges in the field of metabolomics, from study design to metabolite identification.
This course is aimed at PhD students, post-docs and researchers with at least two or three year’s experience in the field of metabolomics who are seeking to improve their skills in metabolomics data analysis. Participants ideally must have working experience using R (including a basic understanding of the syntax and ability to manipulate objects).
Syllabus, Tools and Resources
During this course you will learn about:
•Metabolomics study design, workflows and sources of experimental error, difference between target and un-target approaches.
• Metabolomics data processing tools: hands on open source R based programs, XCMS, MetFrag, MetFusion, rNMR, BATMAN, …
•Metabolomics data analysis: Using R Bioconductor, understanding usage of univariate and multivariate data analysis, data fusion concepts and data clustering …
•Metabolomics downstream analyses: KEGG, BioCyc, MetExplore and Cytoscape for metabolic pathway and network analysis with visualisation of differential expression, understanding metabolomics flux analysis.
•Metabolomics standards and databases: data dissemination and deposition in EMBL- EBI MetaboLights repository, collection and ever growing metabolomics online resource, COSMOS data standards, MSI, …
We will have lively and interactive discussion throughout the course in addition to the hands-on data analysis and processing. We encourage you to bring your data, problems you might have with a particular data set or study for group discussion. You will be asked to present your work and participate in the discussions from day one.
After this course you should be able to…
•Discuss major principles of metabolomics experimental design and factors that impact upon subsequent analysis
•Identify strengths and weaknesses in a variety of metabolomics analytical approaches
•Use a range of Bioinformatics software to pre-process, process and analyse metabolomics data
•Discuss current trends and challenges in metabolomics
|Day 1 - 16 Feb 2015 Chair: Laura Emery|
|13:00||Registration and welcome|
|13:15||Introduction and expectations activity||Laura Emery|
|14:30||Participants flash presentations 2.5 min each||Reza Salek|
|15:30||Work flow and experimental design group activity||Reza Salek|
|17:00||Metabolomics: from experimental design to data analysis – Focus on experimental design||Oscar Yanes|
|17:45||Discussion and problem solving||With Speakers of day|
|18:00||Dissecting the multidisciplinary nature of an untargeted metabolomics workflow||Oscar Yanes|
|Day 2 - 17 Feb 2015 Chair: Reza Salek|
|09:15||Over view of the day|
|09:30||Analysis of LCMS-based metabolomics data: feature detection, grouping, quality control, high-throughput analysis, annotation.||Pietro Francheschi|
|11:30||Analysis of LCMS-based metabolomics data: feature detection, grouping, quality control, high-throughput analysis, annotation.||Pietro Francheschi|
|13:00||Lunch - Poster session|
|14:00||The whole story in real-time: MS data processing and metabolite identification||Steffen Neumann|
|16:00||The whole story in real-time: MS data processing and metabolite identification||Steffen Neumann|
|17:30||Dealing with sparse matrices in high dimensional metabolomic biomarker applications||Michael Eiden|
|18:30||Metabolite identification - Group activity and discussion with problem solving|
|Day 3 - 18 Feb 2015 Chair: Reza Salek|
|09:15||Overview of day||Reza Salek|
|09:30||"Simple" statistics||Ron Wehrens|
|11:00||Break Coffee and discussion|
|11:30||Multivariate statistics - only the brave...||Ron Wehrens|
|14:00||Group activity - energizer||Laura Emery and Reza Salek|
|14:15||Metabolomics data analysis in the context of metabolic networks||Fabien Jourdan|
|15:30||Tea / coffee break|
|16:00||Metabolomics data analysis in the context of metabolic networks||Fabien Jourdan|
|16:45||Special lecture||Rick Higashi|
|17:45||Group activity data analysis discussion + Selected Participant presentation on their datasets||Speakers of day|
|Day 4 - 19 Feb 2015 Chair: Reza Salek|
|09:30||Overview of day||Reza Salek|
|09:45||Data Fusion – Part 1||Age Smilde and Johan Westerhuis (TBC)|
|10:30||Tea / coffee break|
|11:00||Data Fusion – Part 2||Age Smilde and Johan Westerhuis (TBC)|
|11:30||Discussion and Present your fusion Problem||Selected participants|
|14:00||NMR workflow from data processing to metabolite ID||Gwenaelle Le Gall|
|15:30||Tea / coffee break|
|16:00||NMR-based metabolomics data processing and identification using open-source tools||Maria Vinaixa|
|17:45||Group activity discussion + Selected Participant presentation||Data session|
|18:45||Depart conference centre for Course dinner at Cambridge College|
|Day 5 - Date - 20 Feb 2015 Chair: Christoph Steinbeck|
|09:30||Overview of day||Reza Salek|
|09:45||Metabolomics flux introduction||Marta Cascante and Igor Marin De Mas|
|11:30||Metabolomics flux and genome scale||Marta Cascante and Igor Marin De Mas|
|13:45||Metabolomics standards: Where are we now?||Christoph Steinbeck|
|14:15||MetaboLights and data submission||Kenneth Haug/Reza Salek|
|15:30||Metabolomics resources - What we have not covered– Q+A||Reza Salek|
|16:45||Course wrap-up and feedback||Laura Emery|
|17:00||Course closing comments and feedback session|
Application for this course is now closed.
Please note the registration fee for this course will be £200 - it will cover the following:
All meals (breakfast, lunch, dinner and refreshment breaks)
- Accommodation for 4 nights at The Wellcome Trust Conference Centre
- Course materials
- Use of a computer in the EMBL-EBI IT Training Room throughout the course
- Course dinner on Thursday 19th February 2015
There will be a maximum of 30 participants on this course and registration is dependent on selection after successful completion of the application process.
Upon completing the application questions (Items marked * are mandatory) please remember to read the additional information section at the bottom of the page. Only applicants with a complete registration will be considered for the course - incomplete registrations will not be processed.
Applications must be submitted by the 15th December 2014.